kglite 0.9.39

A high-performance graph database library with Python bindings written in Rust

KGLite — Lightweight Knowledge Graph for Python

KGLite is an embedded knowledge graph for Python: pip install, no server, no setup. It speaks Cypher, loads pandas DataFrames, and ships with the connective tissue for AI agents — an MCP server so Claude / Cursor / any MCP-capable LLM can query your graph as a tool, a describe() method that emits a compact XML schema for system prompts, and a code_tree parser that turns any source directory into a graph of functions, classes, calls, imports, decorators, and web-framework routes across 13 languages.

Three storage modes scale from in-memory (millisecond queries on small graphs) to mmap-backed on disk (1 B+ edges, Wikidata-scale). Bundled dataset wrappers turn pip install kglite into a queryable Wikidata or petroleum-domain graph in one line.

Why KGLite?

• Built for LLM agents — describe() XML schema, bundled MCP server, an agent-oriented query surface (cypher(), graph.select(...).traverse(...)), and structural validators (CALL orphan_node({type: ...}) YIELD node) for data-integrity checks that compose with the rest of Cypher.
• One-line public datasets — wikidata.open(path) and sodir.open(path) handle fetch, parallel build, and caching; re-runs reload the cached graph instantly.
• Codebase → graph in one line — kglite.code_tree.build(".") parses Python, Rust, TypeScript, JavaScript, Go, Java, C#, C, C++, Swift, PHP, HTML, and CSS into Function / Class / Module / Route / Element (HTML headings + sections + forms) / Selector (CSS rules) nodes with CALLS / DEFINES / IMPORTS / DECORATES / HANDLES / HAS_CHILD edges. Web-framework route detection ships for Flask, FastAPI, and Django. HTML god-file workflows are first-class: inline <script> blocks are parsed as JS so their functions get CALLS edges, and the document outline surfaces as Element nodes connected via HAS_CHILD. kg.explore(query) does one-call codebase exploration; CALL affected_tests({files: [...]}) returns transitively-impacted test files.
• Scales without leaving Python — in-memory for prototyping, mmap-backed for notebook-scale, disk-mode CSR for graphs too large for RAM. Same API across modes.
• Query with Cypher — MATCH, MERGE, OPTIONAL MATCH, aggregations, parameters, semantic search via text_score().
• DataFrames in, DataFrames out — bulk-load nodes and edges from pandas with add_nodes / add_connections, query results back as DataFrames. End-to-end walkthrough in the Data Loading guide.

How it compares

	KGLite	Kuzu	NetworkX	rustworkx	Neo4j Embedded
Install	pip install kglite	pip install kuzu	pip install networkx	pip install rustworkx	JVM + Java deps
Query language	Cypher (subset)	Cypher (full)	Python API	Python API	Cypher (full)
Storage	in-mem · mmap · disk (1B+ edges)	in-mem · disk (columnar)	in-mem	in-mem	in-mem · disk (JVM)
Bulk-load from pandas	one-liner	via Arrow	manual	manual	via driver
Bundled MCP server for LLM agents	✅	—	—	—	—
describe() schema for LLM prompts	✅	—	—	—	—
Codebase → graph parser	13 languages, route detection	—	—	—	—
Bundled public datasets	Wikidata, Sodir	—	toy graphs only	—	—
License	MIT	MIT	BSD-3	Apache-2	GPLv3

Pick KGLite when you want Cypher + Python ergonomics + LLM-agent plumbing in one wheel. Pick Kuzu for full openCypher coverage and analytical OLAP throughput. Pick NetworkX when you need its enormous graph-algorithm library and your data fits in RAM. Pick rustworkx when you want NetworkX's API in Rust with no query language. Pick Neo4j Embedded when you've standardised on server-mode Cypher and want the in-process driver for tests.

Quick Start

pip install kglite

import pandas as pd
import kglite

# Three storage modes — pick by graph size:
#   default (in-memory)   — small/medium graphs, fastest queries
#   storage="mapped"      — mmap columns, RAM-friendly as you grow
#   storage="disk", path=…  — 100M+ nodes, Wikidata-scale, loaded lazily
graph = kglite.KnowledgeGraph()

# Bulk-load nodes from a DataFrame (also: add_nodes_bulk, from_blueprint,
# load_ntriples, or Cypher CREATE for ad-hoc inserts).
people = pd.DataFrame({
    "id":   ["alice", "bob", "eve"],
    "name": ["Alice", "Bob", "Eve"],
    "age":  [28, 35, 41],
    "city": ["Oslo", "Bergen", "Trondheim"],
})
graph.add_nodes(people, node_type="Person", unique_id_field="id", node_title_field="name")

# Bulk-load relationships the same way (also: add_connections_bulk,
# add_connections_from_source for auto-filter by loaded types).
knows = pd.DataFrame({"src": ["alice", "bob"], "tgt": ["bob", "eve"]})
graph.add_connections(knows, connection_type="KNOWS",
                      source_type="Person", source_id_field="src",
                      target_type="Person", target_id_field="tgt")

# Query — returns a ResultView (lazy; data stays in Rust until accessed).
result = graph.cypher("""
    MATCH (p:Person) WHERE p.age > 30
    RETURN p.name AS name, p.city AS city
    ORDER BY p.age DESC
""")
for row in result:
    print(row['name'], row['city'])

# Or get a pandas DataFrame directly.
df = graph.cypher("MATCH (p:Person) RETURN p.name, p.age ORDER BY p.age", to_df=True)

# Persist to disk and reload.
graph.save("my_graph.kgl")
loaded = kglite.load("my_graph.kgl")

Try it instantly: ready-to-query datasets

Two bundled wrappers turn well-known public sources into queryable graphs without writing a loader. Each call handles the fetch + build + cache cycle, returns a KnowledgeGraph you can cypher() against, and respects a per-dataset cooldown so re-running just loads the cached graph in seconds. KGLite is independent of the upstream organisations — see each module docstring for non-affiliation notes.

Wikidata

Single-stream latest-truthy.nt.bz2 from dumps.wikimedia.org — parallel-decoded with a bit-level block scanner, parsed, built into a queryable graph in one call:

from kglite.datasets import wikidata

g = wikidata.open("/data/wd")                                    # full graph
g = wikidata.open("/data/wd", entity_limit_millions=100)         # 100M slice
g = wikidata.open("/data/wd", storage="memory",                  # in-memory, fast tests
                  entity_limit_millions=10)

Sodir (Norwegian Offshore Directorate)

Petroleum-domain graph from the public ArcGIS REST FeatureServer at factmaps.sodir.no — 33 baseline node types (Field, Wellbore, Discovery, Licence, Stratigraphy, …), ~480 k nodes, parallel-fetched and built in seconds:

from kglite.datasets import sodir

g = sodir.open("/data/sodir")  # in-memory by default; ~30s first run
g = sodir.open("/data/sodir", complement_blueprint="my_extras.json")  # extend

Two-tier cooldown — cheap row-count probes every 14 days; full per-dataset re-fetch every 30 days. Add a complement blueprint to extend the baseline (new node types, custom edges) without touching the canonical schema; the file is persisted into the workdir on first use and auto-loaded after.

Use Cases

Agentic AI — memory and tool use

Give an LLM a structured memory it can query. describe() emits a compact XML schema that fits in a system prompt, and the bundled MCP server exposes the whole graph as a Cypher tool — drop-in for Claude, Cursor, or any MCP-capable agent.

xml = graph.describe()                            # schema for the agent's context
prompt = f"You have a knowledge graph:\n{xml}\nAnswer via graph.cypher()."

# Or serve the whole graph over MCP. `kglite-mcp-server` is shipped
# inside the wheel as a Python console-script entry point — no Rust
# toolchain needed, no PyO3 env vars, no conda env handling.
pip install 'kglite[mcp]'
kglite-mcp-server --graph path/to/graph.kgl

Migrating from a 0.9.18 or 0.9.19 install? No YAML changes needed. pip install --upgrade 'kglite[mcp]' and you're done. The 0.9.20 release retired the bundled Rust binary in favour of a Python entry point, which removes the per-Python-version wheel matrix and the install_name_tool / patchelf / mold complexity that came with it. Cypher execution still happens in the Rust extension module under the GIL release inside cypher(), so performance is unchanged.

Drop a <basename>_mcp.yaml next to the graph to auto-extend the tool surface — source_root: for read/grep/list over your source files, inline Cypher templates as named tools, extensions.embedder for text_score(), extensions.cypher_preprocessor for query rewriting. No fork required for most customisation. See the MCP guide.

Codebase analysis

Parse Python, Rust, TypeScript, Go, Java, C#, and C++ into a graph of functions, classes, calls, and imports. Trace who-calls-what, find dead code, and review structure without leaving your editor. Pairs naturally with the MCP server so an agent can reason over your repo.

from kglite.code_tree import build

graph = build(".")                                # parse current directory
graph.cypher("""
    MATCH (f:Function)-[:CALLS]->(g:Function)
    RETURN g.name, count(f) AS callers
    ORDER BY callers DESC LIMIT 10
""")

RAG retrieval

Store documents, chunks, and entities together as one graph. Combine text_score() semantic similarity with Cypher structure — hybrid retrieval in one query, no second vector DB.

graph.cypher("""
    MATCH (c:Chunk)-[:IN_DOC]->(d:Document)
    RETURN c.text, d.title,
           text_score(c.embedding, $query_vec) AS score
    ORDER BY score DESC LIMIT 5
""", params={"query_vec": query_embedding})

Data exploration and analysis

Load CSVs or DataFrames, walk relationships, run graph algorithms (shortest path, centrality, community detection), and export — all from a notebook.

graph.add_nodes(users_df, node_type="User", unique_id_field="user_id", node_title_field="name")
graph.cypher("""
    MATCH path = shortestPath((a:User {name:'Alice'})-[*]-(b:User {name:'Eve'}))
    RETURN path
""")

Structural validators — surface data-integrity gaps in one query

Six built-in CALL procedures find the gaps that aren't visible from normal queries: nodes with zero edges, missing-required-edge violations, two-step cycles, duplicate titles, more. They compose with the rest of Cypher — feed the output into WHERE, ORDER BY, or downstream aggregation in a single pass.

# Wellbores in our sodir graph that lack a production licence
graph.cypher("""
    CALL missing_required_edge({type: 'Wellbore', edge: 'IN_LICENCE'}) YIELD node
    RETURN node.id, node.title
""")  # 502 violations on the Sodir April-2026 snapshot

# Cross-reference flagged IDs against any query result, in one Cypher pass
graph.cypher("""
    MATCH (l:Licence {title: '057'})<-[:IN_LICENCE]-(w:Wellbore)
    WITH collect(w.id) AS pl057
    CALL missing_required_edge({type: 'Wellbore', edge: 'DRILLED_BY'}) YIELD node
    WHERE node.id IN pl057
    RETURN count(*) AS pl057_missing_drilled_by
""")

missing_required_edge and missing_inbound_edge validate the (type, edge) direction against the graph's actual schema and refuse to execute when misused. See docs/guides/cypher.md for the full procedure list.

Examples

The examples/ directory has runnable, self-contained artifacts covering each of the use cases above:

• codebase_to_claude_mcp.ipynb — clone a famous open-source repo, parse it into a code knowledge graph, run a few Cypher queries, then register a workspace MCP server in Claude Desktop so the agent can repo_management('org/repo') any GitHub repo on demand. End-to-end in ~50 lines.
• open_source_workspace_mcp.yaml — annotated workspace-mode manifest for the github-clone-tracker pattern: agent calls repo_management('org/repo'), kglite clones the repo and builds its code-tree graph, queries flow against the active clone. Drop the file into your workspace directory as workspace_mcp.yaml and run kglite-mcp-server --workspace /path/to/dir/. Walked through in the workspace manifest example.
• legal_graph.py — end-to-end add_nodes / add_connections from pandas DataFrames, covering laws, regulations, and court decisions with citation relationships. The imperative-API alternative when you're building the graph itself, not configuring a server on top.
• code_graph.py — build a code knowledge graph from a source directory via code_tree.build. Produces Function, Class, Module, File nodes with CALLS, DEFINES, IMPORTS edges.
• spatial_graph.py — declarative CSV→graph loading via a JSON blueprint; regions, facilities, and sensors with lat/lon coordinates and pipeline-path traversal queries.
• crates/kglite-mcp-server/ — Rust-native single-binary MCP server (built on rmcp + the mcp-methods framework). Reach for it when the manifest doesn't express what you need; the binary is the reference for layering domain-specific tools on top of the generic source / GitHub / workspace surface.

For Wikidata- and Sodir-scale builds, see the Public datasets section above — kglite.datasets.wikidata.open(...) and kglite.datasets.sodir.open(...) cover those workflows in one call.

Benchmarks

KGLite builds and queries Wikidata-scale graphs on a laptop. Measured with bench/wiki_benchmark.py on an M-series MacBook.

Ingest — full pipeline from compressed N-Triples to a queryable graph:

dataset	triples	nodes	edges	ingest	throughput	peak RAM
wiki100m	100 M	938 K	748 K	29 s	3.4 M triples/s	1.3 GB
wiki500m	500 M	5.6 M	6.7 M	157 s	3.2 M triples/s	5.2 GB
wiki1000m	1 B	14.7 M	15.4 M	395 s	2.5 M triples/s	7.0 GB

Reloading a saved 1 B-triple graph from disk (7 GB on-disk): 3.5 s.

Query latency on the 1 B-triple graph (mapped storage). Type names match the labels Wikidata ships per language — with languages=["en"] (the default), Q5 is renamed to human:

Cypher	wall
MATCH (n)-[:P31]->(:human) RETURN count(n) — typed aggregation	0.5 ms
MATCH (a)-[:P31]->(b)-[:P279]->(c) LIMIT 10 — 2-hop typed	0.9 ms
MATCH (a)-[:P31]->(b {nid:'Q64'}) RETURN a LIMIT 20 — pivot	1 ms
MATCH (a)-[:P31]->(:human) MATCH (a)-[:P27]->(c) LIMIT 10 — join	44 ms

Disk and mapped storage track within 1 % on build; mapped wins on query shapes backed by its in-memory inverted index, disk wins on unbounded typed traversals by staying on sorted-CSR mmap I/O.

No server, no tuning, same Python process as your code.

Key Features

Feature	Description
Cypher queries	MATCH, CREATE, SET, DELETE, MERGE, UNION/INTERSECT/EXCEPT, aggregations (incl. median, percentile_cont, variance), reduce(), ORDER BY, LIMIT, SKIP
Semantic search	Vector embeddings + text_score() for similarity ranking
Text predicates	text_edit_distance, text_normalize, text_jaccard, text_ngrams, text_contains_any / text_starts_with_any for fuzzy match
Graph algorithms	Shortest path (BFS or Dijkstra via weight_property), centrality, community detection, clustering
Structural validators	14 CALL procedures: orphan_node, missing_required_edge, cycle_2step, inverse_violation, transitivity_violation, cardinality_violation, parallel_edges, null_property, type_domain/range_violation, etc. — agent-discoverable integrity checks composable with normal Cypher
Spatial	Coordinates, WKT geometry, distance + containment, geometry primitives (geom_buffer, geom_convex_hull, geom_union/intersection/difference, geom_is_valid, geom_length), kg_knn k-nearest-neighbour
Timeseries	Time-indexed data with ts_*() Cypher functions
Bulk loading	Fluent API (add_nodes / add_connections) for DataFrames
Blueprints	Declarative CSV-to-graph loading via JSON config
Import/Export	Save/load snapshots, GraphML, CSV export
AI integration	describe() introspection, MCP server, agent prompts
Code analysis	Parse codebases via tree-sitter (kglite.code_tree)

Documentation

Full docs at kglite.readthedocs.io:

• Getting Started — installation, first graph, core concepts
• Cypher Guide — queries, mutations, parameters
• Semantic Search — embeddings, vector search
• AI Agents — MCP server, describe(), agent prompts
• API Reference — full auto-generated reference

Requirements

Python 3.10+ (CPython) | macOS (ARM), Linux (x86_64/aarch64), Windows (x86_64) | pandas >= 1.5

License

MIT — see LICENSE for details.